Category Archives: Uncategorized

DataChat: Guided English Language© Ai and ML data analysis

A new spin-off company from the University of Wisconsin-Madison proposes a new interface for data analysis based on Guided English Language© (GEL) to command Artificial Intelligence and Machine Learning methods via “utterances” i.e. English-like phrases easier to write than code whether R, python, SQL, or other traditional tools. The web site is at datachat.ai The… Read More »

Effective and Engaging Scientific Communication Practices

The power of Story telling Scientists often are so deep into their work that they forget to announce the importance of their discovery or their current research to the World! This new (Zoom) online course is meant to help scientists better communicate: 2022 Summer Zoom Course. Here is the content of the course announcement: Effective… Read More »

Nostalgic PAINT app

In 1984 the Macintosh arrived with the amazing MacWrite and MacPaint programs. But at that time it was all in black and white. Later, Windows also had a Paint program. If you feel nostalgic about these programs, there is a (color) version Microsoft Paint online: jspaint.app

TableConvert.com – free tabular data formats converter

This is a repost of my post on the Biochemistry department: tableconvert-com-free-tabular-data-formats-converter Tabular formats When I first came to Madison in 1986 as a postdoc with Biochemistry professor Paul Kaesberg to learn cloning and sequencing, I was surprised when he said that the most important program to work with sequences was the (now defunct GCG) program… Read More »

Bioawk for handling bioinformatics formats

Today I found a new tool: bioawk that was written by Heng Li who also wrote samtools and bwa. I first discovered it ont this blog: bioawk-basics (Bioinformatics Workbooks) There is also a short tutorial on GitHub: github.com/vsbuffalo/bioawk-tutorial I also found a recent docker image, and in fact there are only 2 images on docker hub: lbmc/bioawk updated 2 months ago,… Read More »

A Boy And His Atom: The World’s Smallest Movie

Moving atoms For some reason a paper copy of “Chemical and Engineering News” (November 11, 2019 – Vol 97 Issue 44) ended up in my hands, and I almost missed this fun section named: “30 years of moving atoms: How scanning probe microscopes revolutionized nanoscience” (link.) The article is progressing over time from 1993 til… Read More »

GREP was written overnight – Birth and Name

I use grep very often, and I made-up and acronym that made sense to me: Get REgular ExPression But I discovered this YouTube video that gives an accurate historical recounting of its birth and where its name came  from. See video below, titled “Where GREP Came From – Computerphile” Summary: this comes from the command g/re/p… Read More »

STAR index for human genome – overcoming the hardware barriers

Recently I was testing a Docker image to run a container for Next Gen sequencing, a way to test an existing “pipeline” on the first published study of the effect of the Zika virus. (https://hub.docker.com/r/maayanlab/zika/) Running a docker container may provide some ease in reproducibility, but sometimes there are also hardware barrier that need to… Read More »

Down-sampling FASTQ.gz paired ends

Downsampling I have performed a search for creating a set of down-sampled data from an actual  large dataset, and while there are many creative information on BioStar and other forums, I find that the most versatile and easy to use tool would be one recommended on the forums: seqtk which is available on Github: github.com/lh3/seqtk  Quoting… Read More »